Research workbench

Activity optimized complex I (open form)

Analyse Activity optimized complex I (open form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7DH0
Type: protein
Length: 7,904 residues
Chains: 45
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NADH-ubiquinone oxidoreductase chain 2; NADH-ubiquinone oxidoreductase chain 3…
EC: 7.1.1.2
UniProt: P03892, P03898, P03910, P03902, P03924, P25708, P04394, P15690, P17694, P23709, P42026, P42028, P25712, Q02375, Q02379, P23934, Q02377, Q02370, Q02371, P23935, Q02366, Q05752, P42029, P34943, P34942, Q8HXG6, O97725, Q95KV7, P52505, Q02378, Q02374, Q02365, P48305, Q02380, Q02367, Q02368, Q02369, Q8HXG5, Q02376, Q02827, P03887, P03920, Q02373, Q02372
Ligands: SF4, 3PE, FES, PC1, CDL, FMN, NAP, ZN
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 45 distinct chains · 37% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	NADH-ubiquinone oxidoreductase chain 2 (EC 7.1.1.2)	protein	344	54% helix, 1% strand	P03892
3	NADH-ubiquinone oxidoreductase chain 3 (EC 7.1.1.2)	protein	93	58% helix, 0% strand	P03898
4	NADH-ubiquinone oxidoreductase chain 4 (EC 7.1.1.2)	protein	458	52% helix, 0% strand	P03910
5	NADH-ubiquinone oxidoreductase chain 4L (EC 7.1.1.2)	protein	96	60% helix, 0% strand	P03902
7	NADH-ubiquinone oxidoreductase chain 6 (EC 7.1.1.2)	protein	172	46% helix, 0% strand	P03924
8	NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial (EC 7.1.1.2)	protein	427	31% helix, 8% strand	P25708
9	NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial (EC 7.1.1.2)	protein	207	29% helix, 7% strand	P04394
A	NADH-ubiquinone oxidoreductase 75 kda subunit, mitochondrial (EC 7.1.1.2)	protein	688	21% helix, 13% strand	P15690
B	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial (EC 7.1.1.2)	protein	385	37% helix, 6% strand	P17694
C	NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial (EC 7.1.1.2)	protein	208	17% helix, 21% strand	P23709
D	NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial (EC 7.1.1.2)	protein	152	28% helix, 11% strand	P42026
E	NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial (EC 7.1.1.2)	protein	176	17% helix, 15% strand	P42028
F	NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial	protein	28	18% helix, 0% strand	P25712
G	NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial	protein	123	11% helix, 10% strand	Q02375
H	NADH dehydrogenase [ubiquinone] iron-sulfur protein 5	protein	96	42% helix, 0% strand	Q02379
I	NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial	protein	71	4% helix, 11% strand	P23934
J	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1	protein	69	51% helix, 0% strand	Q02377
K	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2	protein	84	26% helix, 19% strand	Q02370
L	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 3	protein	80	28% helix, 1% strand	Q02371
N	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5	protein	111	47% helix, 0% strand	P23935
O	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6	protein	114	48% helix, 0% strand	Q02366
P	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7	protein	90	7% helix, 3% strand	Q05752
Q	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8	protein	168	35% helix, 1% strand	P42029
R	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial	protein	306	21% helix, 8% strand	P34943
S	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial	protein	319	29% helix, 3% strand	P34942
T	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11	protein	138	59% helix, 0% strand	Q8HXG6
U	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12	protein	132	14% helix, 2% strand	O97725
V	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13	protein	138	43% helix, 0% strand	Q95KV7
W	Acyl carrier protein, mitochondrial	protein	83	46% helix, 0% strand	P52505
X	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1	protein	49	22% helix, 0% strand	Q02378
Y	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, mitochondrial	protein	57	26% helix, 0% strand	Q02374
Z	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3	protein	74	31% helix, 0% strand	Q02365
a	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4	protein	114	44% helix, 0% strand	P48305
b	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial	protein	139	37% helix, 0% strand	Q02380
c	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6	protein	90	33% helix, 0% strand	Q02367
d	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7	protein	107	38% helix, 0% strand	Q02368
f	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9	protein	167	34% helix, 0% strand	Q02369
h	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial	protein	91	37% helix, 0% strand	Q8HXG5
i	NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial	protein	38	71% helix, 0% strand	Q02376
j	NADH dehydrogenase [ubiquinone] 1 subunit C2	protein	113	50% helix, 1% strand	Q02827
1	NADH-ubiquinone oxidoreductase chain 1 (EC 7.1.1.2)	protein	309	58% helix, 0% strand	P03887
6	NADH-ubiquinone oxidoreductase chain 5 (EC 7.1.1.2)	protein	606	61% helix, 1% strand	P03920
g	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	protein	173	42% helix, 1% strand	Q02373
e	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial	protein	141	16% helix, 0% strand	Q02372
M	Acyl carrier protein, mitochondrial	protein	80	41% helix, 0% strand	P52505

Ligands and binding sites

SF4 · Iron/sulfur cluster · ligand · 6 copies · chains 8, A, B, D, E
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains 2, 4, j, T, B, E, L, V, 1
FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains 9, A
PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains 2, 3, S, H, j
CDL · Cardiolipin · ligand · chains 4, b, h, 6
FMN · Flavin mononucleotide · ligand · chains 8
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains D, R
ZN · Zinc ion · metal · chains I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1137	0.88	0.89	98	empty
2	1156	0.87	0.88	120	empty
3	597	0.87	0.92	77	empty
4	511	0.87	0.93	102	empty
5	775	0.86	0.89	90	empty

Interfaces

181 interfaces between chains.

B–C · 2704 Å² buried · 19 hydrogen bonds · protein-protein
8–9 · 2636 Å² buried · 21 hydrogen bonds · protein-protein
3–1 · 2371 Å² buried · 7 hydrogen bonds · protein-protein
5–7 · 2358 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 2156 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

7DH0 · Activity optimized complex I (open form) · the same entry in another collection · chain D against D, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P03892
Every structure of UniProt P03898
Every structure of UniProt P03910
Every structure of UniProt P03902
Every structure of UniProt P03924
Every structure of UniProt P25708
Every structure of UniProt P04394
Every structure of UniProt P15690
Every structure of UniProt P17694
Every structure of UniProt P23709
Every structure of UniProt P42026
Every structure of UniProt P42028
Every structure of UniProt P25712
Every structure of UniProt Q02375
Every structure of UniProt Q02379
Every structure of UniProt P23934
Every structure of UniProt Q02377
Every structure of UniProt Q02370
Every structure of UniProt Q02371
Every structure of UniProt P23935
Every structure of UniProt Q02366
Every structure of UniProt Q05752
Every structure of UniProt P42029
Every structure of UniProt P34943
Every structure of UniProt P34942
Every structure of UniProt Q8HXG6
Every structure of UniProt O97725
Every structure of UniProt Q95KV7
Every structure of UniProt P52505
Every structure of UniProt Q02378
Every structure of UniProt Q02374
Every structure of UniProt Q02365
Every structure of UniProt P48305
Every structure of UniProt Q02380
Every structure of UniProt Q02367
Every structure of UniProt Q02368
Every structure of UniProt Q02369
Every structure of UniProt Q8HXG5
Every structure of UniProt Q02376
Every structure of UniProt Q02827
Every structure of UniProt P03887
Every structure of UniProt P03920
Every structure of UniProt Q02373
Every structure of UniProt Q02372
Elsewhere: RCSB PDB 7DH0 · PDBe 7DH0 · UniProt P03892 · UniProt P03898 · UniProt P03910 · UniProt P03902 · UniProt P03924 · UniProt P25708 · UniProt P04394 · UniProt P15690 · UniProt P17694 · UniProt P23709 · UniProt P42026 · UniProt P42028 · UniProt P25712 · UniProt Q02375 · UniProt Q02379 · UniProt P23934 · UniProt Q02377 · UniProt Q02370 · UniProt Q02371 · UniProt P23935 · UniProt Q02366 · UniProt Q05752 · UniProt P42029 · UniProt P34943 · UniProt P34942 · UniProt Q8HXG6 · UniProt O97725 · UniProt Q95KV7 · UniProt P52505 · UniProt Q02378 · UniProt Q02374 · UniProt Q02365 · UniProt P48305 · UniProt Q02380 · UniProt Q02367 · UniProt Q02368 · UniProt Q02369 · UniProt Q8HXG5 · UniProt Q02376 · UniProt Q02827 · UniProt P03887 · UniProt P03920 · UniProt Q02373 · UniProt Q02372

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